Mercurial > repos > galaxyp > pyteomics_mztab2tsv

comparison mztab_reader.py @ 0:a46d857e25c2 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 49b21b01937067ffc7cf088e615d68177644640b"
author galaxyp
date Fri, 15 Jan 2021 15:57:59 +0000
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children dc31e153fe6c
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-1:000000000000 0:a46d857e25c2
1 #!/usr/bin/env python
2
3 import argparse
4 import os
5
6 import pandas as pd
7 from pyteomics.mztab import MzTab
8
9
10 def read_mztab(input_path, output_path):
11 """
12 Read mztab file
13 """
14 mztab = MzTab(input_path)
15 if mztab.variant == 'P':
16 return read_mztab_p(mztab, output_path)
17 elif mztab.variant == 'M':
18 return read_mztab_m(mztab, output_path)
19
20
21 def read_mztab_p(mztab, output_path):
22 """
23 Processing mztab "P"
24 """
25 mtd = pd.DataFrame.from_dict(mztab.metadata, orient='index')
26 mtd.to_csv(os.path.join(output_path, "mtd.tsv"), sep="\t")
27 prt = mztab.protein_table
28 prt.to_csv(os.path.join(output_path, "prt.tsv"), sep="\t")
29 pep = mztab.peptide_table
30 pep.to_csv(os.path.join(output_path, "pep.tsv"), sep="\t")
31 psm = mztab.spectrum_match_table
32 psm.to_csv(os.path.join(output_path, "psm.tsv"), sep="\t")
33 sml = mztab.small_molecule_table
34 sml.to_csv(os.path.join(output_path, "sml.tsv"), sep="\t")
35
36
37 def read_mztab_m(mztab, output_path):
38 """
39 Processing mztab "M"
40 """
41 mtd = pd.DataFrame.from_dict(mztab.metadata, orient='index')
42 mtd.to_csv(os.path.join(output_path, "mtd.tsv"), sep="\t")
43 sml = mztab.small_molecule_table
44 sml.to_csv(os.path.join(output_path, "sml.tsv"), sep="\t")
45 smf = mztab.small_molecule_feature_table
46 smf.to_csv(os.path.join(output_path, "smf.tsv"), sep="\t")
47 sme = mztab.small_molecule_evidence_table
48 sme.to_csv(os.path.join(output_path, "sme.tsv"), sep="\t")
49
50
51 if __name__ == "__main__":
52 # Create the parser
53 my_parser = argparse.ArgumentParser(description='List of paths')
54 # Add the arguments
55 my_parser.add_argument('--path_in',
56 metavar='path',
57 type=str,
58 required=True,
59 help='the path of input .mztab file')
60 my_parser.add_argument('--path_out',
61 metavar='path',
62 type=str,
63 default=os.getcwd(),
64 help='the path of folder for output .tsv file')
65
66 # Execute parse_args()
67 args = my_parser.parse_args()
68
69 read_mztab(args.path_in, args.path_out)